good morning jason! seems you've bit off quite a chunk there
at any rate, for your question regarding weeding.......what you (or the kids) pull off and throw away is that portion which is NOT part of the design! think weeding the garden and tossing the weeds while keeping the flowers!
the lettering/graphics/numbers that are to be used are left in place on the tacky backing, turned face down then pressed on the garment. be sure to cut your images in reverse!
i'm not familiar with either your plotter or the software that's running it, so i don't know if you will have the ability to contour cut around transfers or not - i'm sure somebody with more experience with your setup will chime in shortly.
good luck!
ps: you realize you'll need a heat press to get reliable results with the thermoflex, right??? a household iron isn't gonna reach the temps you need to permanently fuse it with the fabric.......